AbSciCon day 4: Mars, life, and Mars life


I stepped out of my comfort zone a bit this morning and went to a session on Mars (okay, there weren’t any biology talks). This is far outside of my expertise, so if I say something outrageously wrong, feel free to set me straight in the comments (actually, you can always do that). I’ve never really given up on the idea of life on Mars. I remember the Viking missions and the ambiguous* results of their biological experiments, and I’m still surprised that none of the subsequent robotic missions have followed them up. I think there are better candidates further out in the Solar System, but Mars is a lot easier to get to.

[Read more…]

AbSciCon day 3: the tape of life

When I was in my 20’s, out of college and largely floundering, my dad lent me a paperback copy of Stephen Jay Gould’s Wonderful Life. I had occasionally enjoyed Gould’s column in Natural History, but I lacked the background to understand much beyond that (my undergrad was in political science). Wonderful Life got me interested in evolution, and I started reading other popular books, including more of Gould’s, Dawkins, Simon Conway Morris (the anti-Gould), etc., and pretty soon I found myself in Chris Parkinson‘s lab working on a master’s degree. This is all just to say that this particular book had a big influence on my life, and my first year in Montana was punctuated (see what I did there?) by a trip to Yoho National Park to see the Burgess Shale, the nominal topic of Wonderful Life.

One of the central arguments of Wonderful Life (and others of Gould’s works) was that the outcome of evolution is inherently unpredictable. Contingency, which can be interpreted as true randomness, stochasticity, or sensitive dependence on initial conditions, plays a large role in Gould’s view. Rarely at a loss for a good metaphor, Gould claimed that if “life’s tape” were rewound to some arbitrary time in the past and played again, the outcome would almost certainly be different from the first run.

This idea of ‘rewinding the tape of life’ has become a mainstay of discussions about evolutionary processes. Many of these discussions revolve around the question of how contingent and how deterministic are evolutionary outcomes, and this was the topic of two AbSciCon sessions chaired by Betul Kacar and Rika Anderson.

[Read more…]

AbSciCon day 2

I didn’t make it to many talks yesterday, spending a good part of the day in meetings, including a meeting of the NASA Postdoctoral Program fellows and alumni. The plenary by Nicholas Hud and Rachel Whitaker was fascinating. I’m not sure it lived up to the very ambitious title, “The origin and subsequent evolution of life,” but it did give some ideas about the transition from prebiotic chemistry to cellular life.

Betul Kacar and Rika Anderson’s session “Chance and necessity: from molecules and viruses to cells and populations I” was the most interesting to me. James Cleaves asked and (partly) answered the question ‘is the set of biological molecules on Earth the best or even the only possible set?’ For RNA at least, there are a huge number of closely related, stable molecules that, by all appearances, should operate just as well as the canonical ribosides that all life on Earth actually uses. If so, it would suggest that the particular molecules that polymerize into RNA are more of a ‘frozen accident’ than anything inevitable.

[Read more…]

AbSciCon day 1

Jennifer Pentz, Dinah Davison, and Cristian Solari enjoying a glass of wine.

Jennifer Pentz, Dinah Davison, and Cristian Solari enjoying a glass of wine.

I’m in Chicago for the biennial Astrobiology Science Conference (AbSciCon). This is always (well, it’s my second time) a fun one, with topics ranging from origins of life to proposed interplanetary missions. I took the train from Whitefish, Montana, which is a bit of an adventure in itself.

[Read more…]

African Volvox in Montana

Ninepipe Reservoir

Ninepipe Reservoir near Charlo, MT. Photo by Aeravi.

Last summer, I hosted Drs. Hisayoshi Nozaki, Noriko Ueki, Osami Misumi, and two graduate students from the University of Tokyo, Kayoko Yamamoto and Shota Yamashita, to collect volvocine algae from Montana lakes. To our surprise, we found a species of Volvox (V. capensis) that had previously only ever been found in South Africa! Dr. Nozaki’s team identified the algae collected in Ninepipe Reservoir based on their morphology and DNA sequencing. South Africa and Montana: this is about as disjunct as a distribution can be. Is Volvox capensis a master of long-distance dispersal? Is its distribution actually cosmopolitan, and if so, why hasn’t it ever been found anywhere else?

[Read more…]

Fierce Roller is under attack!

In the last 24 hours, 20 new users registered on the Fierce Roller blog (prior to yesterday, there were 15). Good news, right, expanding readership and all that? In the same 24 hours, there were 35 malicious login attempts, where the previous four weeks had seen 2. All  of the new registrants are from a yahoo.com or .website address, and none of them bothered with a real name. I’m not sure why someone would bother hacking a blog that’s lucky to hit 200 views in a week, but that’s what seems to be happening.

Some time today, I will purge all of these new registrants. If you are a legitimate reader and you get caught up in this, the solution is simple: just email me and tell me you’re a real person.

Chlamy song

Posts may be thin this week. I am preparing a talk for AbSciCon and a manuscript that’s due Monday. Saturday morning, I will board the Empire Builder in Whitefish for a 30-hour ride to Chicago (no doubt some of the manuscript will be written on the train).

Meanwhile, here’s a song about Chlamydomonas (skip to 1:05 if you don’t want to hear the intro).

Pierrick Bourrat responds

[I invited Pierrick Bourrat to respond to my two posts about his new paper and to comments to those posts. He kindly agreed, and he provided the following guest post, which I have edited only for formatting.]

First of all, I would like to thank Matthew Herron for his interest in my work and his invitation to respond to his posts. Also, I would like to thank Rick Michod and Deborah Shelton for their comments.

I will respond to several issues pointed out both in the posts and the comments.

About the usefulness of the export of fitness view of ETI: I agree that it is a useful way of thinking about it, as long as it is used as a heuristic. This means that I am not inclined to think that building models with the assumption that the fitness of a cell would have been 0 had it been in an environment with not social partners will be able to explain in some deep sense ETIs (and even more so the origin of fitness at some level). In his comment to Matthew’s first post, Rick Michod claims that I somehow confuse realized fitness from a more counterfactual notion of fitness.  Well, to be honest, I do not see how one could simulate (I do not mean ‘explain’) the evolution of a process if the variables in the model do not correspond to realized properties of the system. If I want to model a particular phenomenon, I ought to use variables and parameters that represent the target system and clearly, at least for me, this counterfactual notion of fitness does not represent any properties the cells have because they always have social partners. It is common to use expected rather than realized fitness in models, but this assumption is justified when we can assume that population are large and the environment is overall not fluctuating too much. With the counterfactual notion of fitness, aside from being useful for explaining the ETIs, I fail to see how it could be successfully integrated in models (by successfully, I mean how it could represent meaningfully the target system).

[Read more…]

Friday Golden Fleece: America [already] COMPETES

Rep. Lamar Smith

That’s right, he’s the Chairman of the House Committee on Science, Space, and Technology

Imagine (or remember): you’re a grad student; you’ve struggled through your first two years juggling classes, teaching and research; you managed to get your committee together so that you could contend with three weeks of written then three hours of oral comprehensive exams. You synthesized your dissertation proposal and your written comps into something coherent, passed a dozen drafts back and forth with your advisor, and finally managed to navigate the FastLane website to get it submitted to the NSF before the deadline. In all likelihood, it was rejected, so you tried again the following year. One day you’re working at your computer when the lab phone rings, and you’re stunned to find that it’s your program officer telling you that your Doctoral Dissertation Improvement Grant has been funded. $20,000 over two years to support your field work in Bolivia! Some time later, you learn that the Chairman of the U.S. House of Representatives Committee on Science, Space, and Technology is telling the world that your research in particular is a waste of taxpayer money.

[Read more…]

Expression and form: Arash Kianianmomeni on gene regulation

Kianianmomeni Figure 1

Figure 1 from Kianianmomeni 2015. Gene regulatory mechanisms behind the evolution of multicellularity. Model illustrating the role of gene regulatory mechanisms in the evolution of multicellular Volvox from a Chlamydomonas-like ancestor.

Arash Kianianmomeni’s latest paper in Communicative & Integrative Biology addresses the possible roles of gene regulation and alternative splicing in the evolution of multicellularity and cellular differentiation (Kianianmomeni, A. 2015. Potential impact of gene regulatory mechanisms on the evolution of multicellularity in the volvocine algae. Commun. Integr. Biol., 37–41. doi 10.1080/19420889.2015.1017175). The article is an ‘Addendum’ to a 2014 study by Kianianmomeni and colleagues in BMC Genomics. Communicative & Integrative Biology often invites authors to write these addenda after they have published a (usually high impact) paper elsewhere, providing authors the opportunity to publish material that was not included in the original paper due to space limitations or because it was opinionated or speculative. I may address the BMC Genomics article in a future post, but right now there is more new volvocine research than I have time to write about (it should be an exciting Volvox meeting this summer!).

[Read more…]